Mass spectrometry has become the enabling tool for identification of both lipids and proteins and for determination of their structures and properties. The changes in lipids with disease have become increasingly recognized, suggesting they may be biomarkers. One goal of the Washington University Mass Spectrometry Research Resource is to build a foundation for understanding lipid fragmentation, facilitating both de novo and computer-assisted identification of increasingly complex lipids found in decreasing amounts in bacteria and parasites. This work will continue because we recognize the growing challenge to identify more complex lipids and to uncover their role in infection and disease. In protein science and proteomics, related challenges exist to understand, with greater speed and sensitivity, protein properties and interactions. As a second goal, various chemical footprinting procedures that take advantage of the separation and analysis capabilities of modern chromatography and mass spectrometry will be explored as sources of information on protein structure, folding, and interfaces with metal ions, DNA, and other proteins. The strategy is to build a "tool box" of footprinting reagents that overtly modify proteins to map those regions that are accessible to reaction, thereby revealing interfaces and quantifying affinities. This approach takes full advantage of the power of modern "bottom-up" proteomics and is designed to be exportable to any proteomics laboratory. Nevertheless, bottom-up analytical proteomics fails when confronted with the need to identify the complex arrays of protein modifications that often form in post-translational modification or are introduced by footprinting. Addressing this problem by improving top-down proteomics is the third goal of the WU Resource. We propose to develop new instrumentation, methods, and associated data processing and interpretation strategies. They will be implemented along with a new high-field Fourier transform ion cyclotron resonance mass spectrometer to aid biomedical researchers with problems for which protein modification is an issue. Its success will serve to demonstrate a paradigm for top-down sequencing that can be employed by other researchers who search for the fine details of protein structure and function.